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I've had a very similar issue, and so I decided to compile several methods for solving it. So, following, there are those options and some of them I got from the answers already provided here. I understand this is a little bit offtopic from the question, but it's in tune with the answers. This has many parts and those are all softwares I could try myself ...

Disk Inventory X is another excellent disk space visualizer.
FileVault or any other third party software is not necessary at fault here.
Mac OS X is simply a complex and modern operating system that uses disk space is dynamic and often unpredictable ways. Not only does the swapfile grows and shrinks but OS X also has a sub system that creates a Dynamic ...

Download and run GrandPerspective for a nice graphical view of what's occupying disk space -- something like this:
Run this before and after the reboot and you should be able to see what the big differences are.

Every time you make the computer do something extra, in this case encrypting/decrypting all file access, it will take longer and the machine will slow down a bit.
File Vault 1 did slow things down noticeably, but with File Vault version 2 (Introduced in OS X 10.7 (Lion)) running on an SSD there is not noticeable decrease in reading or writing files. I have ...

No, it's not. Some say it's a benefit if you have geo-location and remote wipe configured (or other similar software) as it increases the chance that someone finding the Mac will connect it to the Internet.
What's happening is that you also have Find My Mac on. That enables a Safari-only guest account which will allow users to log in and run Safari. The ...

John Siracusa's detailed Lion review covers the new FileVault disk encryption feature in great detail:
http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13#lion-file-system
To summarise, the new system is "volume" based. This means that not all volumes can be or are encrypted. The Lion recovery partition for example is not encrypted. Non Mac ...

Yes. FileVault2 is volume based so you can have an encrypted Mac OS volume and an unencrypted Windows bootcamp partition for instance. The Recovery partition is also not encrypted.
FileVault2 requires Lion to decrypt/decode the drive. It doesn't work with Windows Linux, or previous versions of Mac OS X. I recommend John Siracusa's Lion review for more ...

There are a number of possible pitfalls to having an encrypted home folder; most of them are more-or-less intrinsic to the idea, so they're not likely to go away... ever.
UPDATE: Lion's FileVault 2 uses full-volume encryption rather than just home-directory, so it actually does make some of these issues go away and changes several others. I've added notes ...

Encryption happens on-the-fly. If the data was written to the hard drive, then passed through an encryption algorithm that then deleted the written data and re-wrote it, encrypted, that would be hella inefficient, and would largely defeat the purpose. I think the answer to your question is no, but of course remember that if you're going from a data set ...

Password less 'Guest' accounts can no longer be created since the whole disk is encrypted than just the User's home directory. It's sad that I could not find any information on the kb article in Apple about this.

Your question contains the most important thing needed to secure a computer against a motivated attack to compromise a FileVault 2 protected Mac volume.
Don't connect FireWire to a device you don't or can't trust while you are logged in to an account that has file vault keys active.
Pick good single use passwords to reduce the chance of other compromises ...

No, the backups will not be encrypted automatically, but it's very easy to enable for directly attached disks. Just check "Encrypt Backup Disk" in the Time Machine disk selection settings.
If you're backing up to another Mac, you can use Disk Utility on that Mac to erase non-boot drives and put an encrypted partition on them:

Nope, you can’t. When FileVault is enabled, the disk needs to be decrypted on every boot. As the computer can’t access files on the disk, It generates a simple login screen so that you can enter your password and decrypt the disk. This UI is hardcoded into the firmware of your computer, and can’t be changed.
Source: ...

If you hover over the disabled option, a tooltip appears explaining that the guest account can't be activated with FileVault turned on:
This is because the new FileVault uses full-disk encryption that's decrypted by the login password of one of the users. As the guest account, by its nature, does not have a password, that would leave your computer ...

It's not possible (at least not that I know) to specify Filevault's target dir. It will work by automatically working with your home folder by creating (if you are in Leopard or above) a Sparse Bundle (or a Sparse Disk Image if you are in Tiger). The reason for the change has to do with Time Machine (and to allow -to a certain extent- to backup a FileVaulted ...

After a bit of messing about, it turns out that there is a better compromise which doesn't seem to be clearly documented anywhere obvious, so I thought I'd share it here. I don't believe this is a duplicate but I'm happy to see this question closed if I've missed something.
The cost of the solution (which may be unacceptable to some) is that you need to ...

The new Filevault seems to put far fewer constraints on you than the old version. You don't have to log out for time machine to work, for example, and all the sharing daemons appear to work fine (some of them were disabled when filefault was enabled if I recall correctly. I think web sharing was among them, which made my laptop a bit useless as a ...

Borrowing heavily from John Siracusa's Lion review...
FileVault 2 is a Whole Disk Encryption system, as opposed to just a 'store your home folder in an encrypted disk image' solution. It's implemented as a filesystem layer below the actual volume that you unlock at system boot time. If you're familiar with LVM, it's much the same way. Whenever you get past ...

If you're using the Lion's built-in encryption, the answer is yes. You can just work with the disk as usual, and the encryption happens in the background, even if you restart the Mac.
In Terminal.app, you can check the encryption status with
diskutil cs list

Just found the answer here. Basically, from the terminal, type:
sudo diskutil cs list
You'll get a list of your drives and a bunch of related info. Look for the one you want to format and grab its Logical Volume Group's UUID. It should look something like this:
Logical Volume Group XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
Then erase the drive by executing ...

Encrypt the startup volume with Core Storage without FileVault
Two days after I added this answer, Apple published a technical white paper: Best Practices for Deploying FileVault 2 – Deploying OS X Full Disk Encryption Technology (PDF). At a glance, some of what I describe below seems to be described by Apple as:
Disk Password—based DEK.
Preparation
...

This is much easier to do beginning in Mavericks. The fdesetup command was expanded to support recovery key changes and verification.
sudo fdesetup validaterecovery will prompt you for the key, which should be entered in all caps with the hyphens.

CPU load
Filevault 2 supports Intel® Advanced Encryption Standard (AES). It's important to know if your Mac has an Intel processor which supports this, as it significantly reduces the CPU overhead. Search for you CPU here an look if is supports the New AES instructions.
My Macbook Pro 2011 got this feature enabled via a firmware update (Apple did not ...

Do you run the risk of loosing your computer? Is the information stored on your computer of high value to other persons?
If your answer is no to these questions you should not consider using FileVault 2 as it has some drawbacks:
The encryption happens on the fly. As your C2D processor does not support hardware accelerated encryption, your CPU load will ...

(I'm assuming you are referring to FileVault 2 found in OS X Lion)
The folks at AnandTech have run some performance benchmarks on the new FileVault. Quote:
... [described are several I/O tests with and without FileVault enabled, including some charts you might want to have a look at] ...
Overall the hit on pure I/O performance is in the 20 - 30% ...

No, Windows does not support FileVault (so it would not boot if it was encrypted thus!) The Windows option would be BitLocker.
(perhaps it is more correct to say FileVault does not support anything but Mac OS Extended (Journaled) partitions)
If you need a great, free, cross-platform, open-source, strong encryption tool check out TrueCrypt.
Can you use ...